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Rosetta
2021.16
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Rosetta
2021.16
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#include <PrecomputedPairEnergiesInteractionGraph.hh>
Public Member Functions | |
| ~PrecomputedPairEnergiesInteractionGraph () override | |
| PrecomputedPairEnergiesInteractionGraph (int num_nodes) | |
| void | add_to_two_body_energies_for_edge (int node1, int node2, ObjexxFCL::FArray2< core::PackerEnergy > const &res_res_energy_array, bool const use_threadsafe_method=false) |
| interface for PrecomputedPairEnergiesEdge::add_to_two_body_energies More... | |
| void | add_to_two_body_energies_for_edge (int node1, int node2, int state_node1, int state_node2, core::PackerEnergy const two_body_energy) |
| interface to PrecomputedPairEnergiesEdge::add_to_two_body_energies More... | |
| void | set_two_body_energy_for_edge (int node1, int node2, int state_node1, int state_node2, core::PackerEnergy const two_body_energy) |
| interface to PDEdge::set_two_body_energy More... | |
| void | clear_two_body_energy_for_edge (int node1, int node2, int state_node1, int state_node2) |
| interface to PDEdge::clear_two_body_energy More... | |
| void | set_twobody_energies_multithreaded (std::pair< core::Size, core::Size > const &nodes, std::pair< core::pack::rotamer_set::RotamerSetCOP, core::pack::rotamer_set::RotamerSetCOP > rotsets, core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, basic::thread_manager::RosettaThreadAssignmentInfo const &thread_info, bool const finalize_edges, core::conformation::symmetry::SymmetryInfoCOP symminfo, std::pair< core::Size, core::Size > const &resids, bool const do_orient, bool const symmetric_swap) |
| Given two nodes, compute the energy of all interacting rotamers and add those energies to the edge between the nodes. This is suitable for use in a multithreaded context. More... | |
| void | add_longrange_twobody_energies_multithreaded (std::pair< core::Size, core::Size > const &nodes, std::pair< core::pack::rotamer_set::RotamerSetCOP, core::pack::rotamer_set::RotamerSetCOP > rotsets, core::pose::Pose const &pose, core::scoring::methods::LongRangeTwoBodyEnergyCOP lr_energy, core::scoring::ScoreFunction const &sfxn, basic::thread_manager::RosettaThreadAssignmentInfo const &thread_info, bool const finalize_edges, core::conformation::symmetry::SymmetryInfoCOP symminfo, std::pair< core::Size, core::Size > const &resids, bool const do_orient, bool const symmetric_swap) |
| Given two nodes and a long-range energy, compute the long-range energy of all interacting rotamers and add those energies to the edge between the nodes. This is suitable for use in a multithreaded context. More... | |
| virtual void | declare_edge_energies_final (int node1, int node2, bool const use_threadsafe_lookup=false) |
| call this if you're done storing energies in an edge - it will reduce the memory usage for that edge if possible More... | |
 Public Member Functions inherited from core::pack::interaction_graph::FixedBBInteractionGraph | |
| ~FixedBBInteractionGraph () override | |
| FixedBBInteractionGraph (int num_nodes) | |
| virtual int | get_num_aatypes () const =0 |
| virtual bool | aa_submatrix_energies_retrievable () const |
| virtual int | aatype_for_node_state (int node_ind, int node_state) const |
| virtual ObjexxFCL::FArray2D < core::PackerEnergy > | get_aa_submatrix_energies_for_edge (int node1, int node2, int node1aa, int node2aa) const |
| void | set_sparse_aa_info_for_edge (int node1, int node2, ObjexxFCL::FArray2_bool const &sparse_conn_info) |
| interface to PDEdge::set_sparse_aa_info More... | |
| bool | get_sparse_aa_info_for_edge (int node1, int node2, int node1aa, int node2aa) |
| returns true if node1aa and node2aa are amino acid neighbors More... | |
| void | force_aa_neighbors_for_edge (int node1, int node2, int node1aa, int node2aa) |
| interface to FixedBBEdge::force_aa_neighbors More... | |
| void | force_all_aa_neighbors_for_edge (int node1, int node2) |
| interface to PDEdge::force_aa_neighbors More... | |
| virtual core::PackerEnergy | get_two_body_energy_for_edge (int node1, int node2, int state_node1, int state_node2) const |
| interface to FixedBBEdge::get_two_body_energy More... | |
| Public Member Functions inherited from core::pack::interaction_graph::InteractionGraphBase | |
| ~InteractionGraphBase () override | |
| destructor More... | |
| InteractionGraphBase (int num_nodes) | |
| main constructor More... | |
| int | get_num_nodes () const override |
| Get the number of nodes in the graph. More... | |
| virtual void | initialize (pack_basic::RotamerSetsBase const &rot_sets)=0 |
| void | set_num_states_for_node (int node, int num_states) |
| sets the number of states for a node of a particular index NEW REQUIREMENT: Nodes must have their num-states set in ascending order by node index; that is, node 1 must go first, node 2 next, and so on. More... | |
| int | get_num_states_for_node (int node) const override |
| returns the number of states for a particular node More... | |
| int | get_num_total_states () const override |
| Get the total number of states. More... | |
| virtual core::PackerEnergy | get_one_body_energy_for_node_state (int node, int state)=0 |
| void | add_edge (int node1, int node2) |
| creates a new edge between nodes index1 and index2. Nodes do not have to be listed in order More... | |
| bool | get_edge_exists (int node1, int node2) const |
| returns true if an edge between node1 and node2 exists More... | |
| void | drop_all_edges_for_node (int node) |
| deletes all edges adjacent to the node specified More... | |
| void | print_vertices () const |
| calls print() on each of the nodes in the graph More... | |
| virtual void | print () const |
| void | output_connectivity (std::ostream &os) const |
| writes out a list of all the edges in the graph More... | |
| void | output_dimacs (std::ostream &os) const |
| writes out a connectivity description of the graph in the famous dimacs format. (where the first column "DIMACS:" should be sed'ed out) More... | |
| void | set_onebody_energies_multithreaded (core::Size const node_index, core::pack::rotamer_set::RotamerSetCOP rotset, core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, basic::thread_manager::RosettaThreadAssignmentInfo const &thread_assignments) |
| Compute and store the onebody energy for all rotamers at a position. Safe for a multithreaded context. More... | |
| void | prepare_graph_for_simulated_annealing () override |
| iterate across edges and nodes and allow them to prepare for simulated annealing More... | |
| void | blanket_assign_state_0 () override=0 |
| State initialization. More... | |
| core::PackerEnergy | set_state_for_node (int node_ind, int new_state) override=0 |
| Explicit state modification for a node. More... | |
| core::PackerEnergy | set_network_state (ObjexxFCL::FArray1_int &node_states) override=0 |
| Explicit state modification for the network. More... | |
| void | consider_substitution (int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_node) override=0 |
| Consider switching node "node_ind" to state "new_state". More... | |
| core::PackerEnergy | commit_considered_substitution () override=0 |
| Accept a considered substitution (i.e. make the substitution permanent; commit it). More... | |
| core::PackerEnergy | get_energy_current_state_assignment () override=0 |
| Get the energy resulting from the current set of state assignments. More... | |
| void | set_edge_weight (int node1, int node2, Real edge_weight) |
| Real | get_edge_weight (int node1, int node2) const |
| virtual int | get_edge_memory_usage () const =0 |
| virtual void | print_current_state_assignment () const =0 |
| void | set_errorfull_deltaE_threshold (core::PackerEnergy deltaE) override=0 |
| Set an error threshold. More... | |
| bool | any_vertex_state_unassigned () const override |
| Returns true if any node in the graph is in state 0, the unassigned state. More... | |
| void | add_to_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &one_body_energies) |
| takes one FArray of energies – one energy for each state for each node More... | |
| void | update_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &old_energy1b, ObjexxFCL::FArray1< core::PackerEnergy > &new_energy1b) |
| decrements the one body energies by the values held in old_energy1b, increments the one body energies by the values held in new_energy1b, and copies new_energy1b into old_energy1b. More... | |
| void | zero_one_body_energies_for_node (int node) |
| void | add_to_nodes_one_body_energy (int node_ind, utility::vector1< core::PackerEnergy > const &one_body_energies) |
| void | add_to_nodes_one_body_energy (int node_ind, ObjexxFCL::FArray1< core::PackerEnergy > const &one_body_energies) |
| void | add_to_nodes_one_body_energy (int node_ind, int state_id, core::PackerEnergy const one_body_energy) |
| interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy More... | |
| void | set_number_of_energy_sum_vertex_groups (int num_groups) |
| a user may define subsets of the vertex set for which they would like to know the internal energy sum. For instance in a graph with 6 vertices, {a,b,c,d,e,f} a user may be interested in the sum of the one- and two-body energies for vertices {a,b,c}. The graph will return sum of the one body energies for vertices a b and c and also any two-body energies for the edges in the subgraph induced by a,b, and c. (In this case, edges {a,b}, {a,c} and {b,c} if these edges are part of the graph. The edge {a,d} will not be counted if it is part of the graph.) More... | |
| void | set_vertex_member_of_group (int vertex, int group) |
| a user may define subsets of the vertex set for which they would like to know the internal energy sum. For instance in a graph with 6 vertices, {a,b,c,d,e,f} a user may be interested in the sum of the one- and two-body energies for vertices {a,b,c}. The graph will return sum of the one body energies for vertices a b and c and also any two-body energies for the edges in the subgraph induced by a,b, and c. (In this case, edges {a,b}, {a,c} and {b,c} if these edges are part of the graph. The edge {a,d} will not be counted if it is part of the graph.) More... | |
| void | print_vertex_groups () |
| virtual core::PackerEnergy | get_energy_sum_for_vertex_group (int group_id)=0 |
| int | count_connected_components_and_initialize_vertex_groups () |
| makes a depth first traversal of the graph, counting the number of connected components, and initializes the vertex group memberships to reflect the connected components. Returns the number of connected components in the graph. More... | |
| void | note_vertex_reached (int node_index) |
| marks a vertex as belonging to the connected component currently being traversed in the depth first traversal. More... | |
| bool | vertex_already_reached (int node_index) |
| used by class NodeBase during the depth-first traversal to determine the number of connected components in the graph. returns true if the dft has already reached the node. More... | |
| bool | get_vertex_member_of_energy_sum_group (int node_index, int group_id) |
| virtual unsigned int | getTotalMemoryUsage () const |
| void | reset_edge_list_iterator_for_node (int node_index) const |
| set the Graph's (single) edge list iterator to the beginning of the edge list for a particular node More... | |
| void | increment_edge_list_iterator () const |
| increment the (single) edge list iterator to the next element More... | |
| bool | edge_list_iterator_at_end () const |
| test: have we arrived at the edge list end? More... | |
| EdgeBase const & | get_edge () const |
| return a const reference to an edge pointed at by the list iterator More... | |
| virtual void | declare_all_edge_energies_final () |
| Iterates over all edges and calls declare_energies_final() on all of them. Takes O(N) time, where N is the number of edges. More... | |
| EdgeBase const * | find_edge (int node1, int node2, bool const use_threadsafe_lookup=false) const |
| Find an edge and return a const pointer to it. More... | |
| EdgeBase * | find_edge (int node1, int node2, bool const use_threadsafe_lookup=false) |
| Find an edge and return a nonconst pointer to it. More... | |
| virtual NodeBase * | create_new_node (int node_index, int num_states)=0 |
| virtual EdgeBase * | create_new_edge (int index1, int index2)=0 |
| NodeBase * | get_node (int index) const |
| int | get_num_edges () const |
| std::list< EdgeBase * >::iterator | get_edge_list_begin () |
| std::list< EdgeBase * >::iterator | get_edge_list_end () |
| std::list< EdgeBase * > ::const_iterator | get_edge_list_begin () const |
| std::list< EdgeBase * > ::const_iterator | get_edge_list_end () const |
| Public Member Functions inherited from core::pack::interaction_graph::AnnealableGraphBase | |
| AnnealableGraphBase () | |
| Constructor. More... | |
| AnnealableGraphBase (AnnealableGraphBase const &src) | |
| Copy constructor. More... | |
| ~AnnealableGraphBase () override | |
| Destructor. More... | |
| virtual void | clean_up_after_packing (core::pose::Pose &pose) |
| Provide the opportunity for an AnnealableGraph to clean up cached data in the pose or inside itself after packing. More... | |
Additional Inherited Members | |
| Protected Member Functions inherited from core::pack::interaction_graph::FixedBBInteractionGraph | |
| FixedBBNode const * | get_fixedbb_node (int node_index) const |
| Downcasts. More... | |
| FixedBBNode * | get_fixedbb_node (int node_index) |
| FixedBBEdge const * | get_fixedbb_edge (int node1, int node2) const |
| FixedBBEdge * | get_fixedbb_edge (int node1, int node2) |
| Protected Member Functions inherited from core::pack::interaction_graph::InteractionGraphBase | |
| void | clean_up_edges_marked_for_deletion () |
| Remove those edges that have marked themselves for deletion. More... | |
| virtual unsigned int | count_static_memory () const =0 |
| virtual unsigned int | count_dynamic_memory () const |
| void | drop_edge (std::list< EdgeBase * >::iterator edge) |
| removes edge from edge list at iterator iter More... | |
| int | get_node_state_offset (int index) const |
| bool | mine (EdgeBase const *edge) const |
|
inlineoverride |
|
inline |
| void core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::add_longrange_twobody_energies_multithreaded | ( | std::pair< core::Size, core::Size > const & | nodes, |
| std::pair< core::pack::rotamer_set::RotamerSetCOP, core::pack::rotamer_set::RotamerSetCOP > | rotsets, | ||
| core::pose::Pose const & | pose, | ||
| core::scoring::methods::LongRangeTwoBodyEnergyCOP | lr_energy, | ||
| core::scoring::ScoreFunction const & | sfxn, | ||
| basic::thread_manager::RosettaThreadAssignmentInfo const & | thread_info, | ||
| bool const | finalize_edges, | ||
| core::conformation::symmetry::SymmetryInfoCOP | symminfo, | ||
| std::pair< core::Size, core::Size > const & | resids, | ||
| bool const | do_orient, | ||
| bool const | symmetric_swap | ||
| ) |
Given two nodes and a long-range energy, compute the long-range energy of all interacting rotamers and add those energies to the edge between the nodes. This is suitable for use in a multithreaded context.
The edge must already exist. The "do_orient" and "symmetric_swap" inputs are only used in the symmetric case, and only control the generation of temporary, oriented rotamersets from rotsets.
The edge must already exist. The "do_orient" and "symmetric_swap" inputs are only used in the symmetric case, and only control the generation of temporary, oriented rotamersets from rotsets.
References core::pack::rotamer_set::symmetry::SymmetricRotamerSets::orient_rotamer_set_to_symmetric_partner(), core::scoring::ScoreFunction::prepare_rotamers_for_packing(), TR(), and core::scoring::ScoreFunction::weights().
| void core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::add_to_two_body_energies_for_edge | ( | int | node1, |
| int | node2, | ||
| ObjexxFCL::FArray2< core::PackerEnergy > const & | res_res_energy_array, | ||
| bool const | use_threadsafe_method = false |
||
| ) |
interface for PrecomputedPairEnergiesEdge::add_to_two_body_energies
| void core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::add_to_two_body_energies_for_edge | ( | int | node1, |
| int | node2, | ||
| int | state_node1, | ||
| int | state_node2, | ||
| core::PackerEnergy const | two_body_energy | ||
| ) |
interface to PrecomputedPairEnergiesEdge::add_to_two_body_energies
| node1 | - [in] - the index of the smaller-indexed node |
| node2 | - [in] - the index of the larger-indexed node |
| state_node1 | - [in] - state on smaller-indexed node |
| state_node2 | - [in] - state on larger-indexed node |
| two_body_energy | - [in] - the energy for this state pair |
| void core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::clear_two_body_energy_for_edge | ( | int | node1, |
| int | node2, | ||
| int | state_node1, | ||
| int | state_node2 | ||
| ) |
interface to PDEdge::clear_two_body_energy
| node1 | - [in] - the index of the smaller-indexed node |
| node2 | - [in] - the index of the larger-indexed node |
| state_node1 | - [in] - state on smaller-indexed node |
| state_node2 | - [in] - state on larger-indexed node |
|
virtual |
call this if you're done storing energies in an edge - it will reduce the memory usage for that edge if possible
| node1 | - [in] - the index of the smaller-indexed node |
| node2 | - [in] - the index of the larger-indexed node |
| use_threadsafe_lookup | - [in] - If true, we don't cache the last edge found for faster future lookups. False by default. |
References core::pack::interaction_graph::EdgeBase::declare_energies_final().
| void core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::set_two_body_energy_for_edge | ( | int | node1, |
| int | node2, | ||
| int | state_node1, | ||
| int | state_node2, | ||
| core::PackerEnergy const | two_body_energy | ||
| ) |
interface to PDEdge::set_two_body_energy
| node1 | - [in] - the index of the smaller-indexed node |
| node2 | - [in] - the index of the larger-indexed node |
| state_node1 | - [in] - state on smaller-indexed node |
| state_node2 | - [in] - state on larger-indexed node |
| two_body_energy | - [in] - the energy for this state pair |
| void core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::set_twobody_energies_multithreaded | ( | std::pair< core::Size, core::Size > const & | nodes, |
| std::pair< core::pack::rotamer_set::RotamerSetCOP, core::pack::rotamer_set::RotamerSetCOP > | rotsets, | ||
| core::pose::Pose const & | pose, | ||
| core::scoring::ScoreFunction const & | sfxn, | ||
| basic::thread_manager::RosettaThreadAssignmentInfo const & | thread_info, | ||
| bool const | finalize_edges, | ||
| core::conformation::symmetry::SymmetryInfoCOP | symminfo, | ||
| std::pair< core::Size, core::Size > const & | resids, | ||
| bool const | do_orient, | ||
| bool const | symmetric_swap | ||
| ) |
Given two nodes, compute the energy of all interacting rotamers and add those energies to the edge between the nodes. This is suitable for use in a multithreaded context.
The edge must already exist. The "do_orient" and "symmetric_swap" inputs are only used in the symmetric case, and only control the generation of temporary, oriented rotamersets from rotsets.
The edge must already exist. The "do_orient" and "symmetric_swap" inputs are only used in the symmetric case, and only control the generation of temporary, oriented rotamersets from rotsets.
References core::scoring::ScoreFunction::any_lr_residue_pair_energy(), core::scoring::ScoreFunction::evaluate_rotamer_pair_energies(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::orient_rotamer_set_to_symmetric_partner(), core::scoring::ScoreFunction::prepare_rotamers_for_packing(), and TR().
1.8.7